Always thrifty, Pinkerton thought that he could save some money by not paying someone else for poles to make barrel hoops. Before long, he found a small deserted island in the middle of the Fox River and rowed out to cut down a supply of his own. However, when he got to the island he found signs that someone had been there and knowing that counterfeiters had been working in the area, he wondered if the island might be their hideout.

When he returned, he notified the local sheriff of his suspicions and the two teamed up to stake out the island which soon led to the arrest of the counterfeit band. However, they failed to catch the ringleader. Soon, Pinkerton found himself involved in the search for the leader and soon tracked him down, as well.

This accidental involvement in justice led to Pinkerton’s appointment as a deputy sheriff for Kane County and in 1850 he became Chicago's first police detective. That same year, he, along with Chicago attorney, Edward Rucker, founded, the North-Western Police Agency.

In the meantime, Allan's brother, Robert, had his formed his own business called "Pinkerton & Co" as early as 1843. Robert's organization was originally established as a railroad contractor, but somewhere along the line, he began to work as a  railroad detective. Through his contacts in the railroad business, Robert had also secured a number of contracts with Wells Fargo to provide guards on stage coaches. Robert's business grew so rapidly that he hired several men as railroad and stage coach detectives and guards.

When Allan and Rucker's business dissolved a year after it was formed, Allan joined his brother Robert in his already established company and the name was changed to the Pinkerton National Detective Agency. The "new" company provided a variety of detective services, from private military contractors to security guards, but specialized in the capture of counterfeiters and train robbers. Though there were a few other detective agencies at the time, most had unsavory reputations and the Pinkerton Agency was the first to set uniform fees and establish practices which quickly earned respect for the organization.

In 1861, while investigating a railway case, the agency uncovered an assassination plot against Abraham Lincoln, where conspirators intended to kill Lincoln in Baltimore during a stop on his way to his inauguration. However, with Pinkerton’s warning, Lincoln's itinerary was changed. During the Civil War, President Lincoln hired the Pinkerton Detective Agency to organize a “secret service” to obtain military information on the Confederates and sometimes act as Lincoln's bodyguard. Working diligently, Allan Pinkerton traveled under the pseudonym of "Major E.J. Allen."